Plot Profile Question

Is there any way to generate a plot profile that uses the %area instead of average intensity? I’m trying to extrapolate the number of axons in an image, and this information needs to come from the area that has signal, not how strong the signal is.


Hi Abernst,

Here’s a suggestion.

  1. Threshold the image so that you have an image with 255 intensity for axons and 0 for not-axons. There’s a range of automatic thresholds or you can set it by hand.

  1. Go to Process > Math > Divide and the image by 2.55. . This makes the pixel value 100 for axons.

  2. Double click on the line tool and make it quite wide so it’s averaging over wide area (otherwise you’ll just yet 0 and 100 in the plot.

  3. Plot the profiles, the y axis will be percentage of axons along the line. Below is a comparison for the original image and the threshold one:

Hope it helps,


Hi Chris,
Thank you for your reply. Unfortunately, when I threshold the image I end up with a value that is much higher than the actual number of axons I get when manually counting. If I do a plot of the entire image without thresholding, for some reason it is much closer. Do you know why that is?